OncoLand Case Study - Summarize Mutation Count

From Array Suite Wiki

Summarize per-sample and per-tumor mutations across multiple genes

Summarizing mutation frequencies within a protein complex, members of a pathway, or even across the genome, can give insights into differences between tumors. You can explore mutation frequencies at multiple levels with TCGALand analytics and Array Studio analysis and visualization functions.

Identify samples with mutations in the Swi/Snf complex

The Swi/Snf genes encode members of a protein complex that can remodel chromatin; mutations in members of the complex have been linked to various cancers. TCGALand can be queried for samples containing mutations in one or more Swi/Snf members.



Visualize differences in Swi/Snf complex mutations using Array Studio

After counting the per-sample mutation load for the Swi/Snf complex, we can use Array Studio's summarization methods to reveal the percent of samples in each tumor that are mutated for at least one Swi/Snf member.



Visualize differences in Swi/Snf complex mutations using TCGALand Views

Array Studio's analysis and summary functions can be used to summarize the per-tumor mutation frequency for one or more genes, such as Swi/Snf complex members. However, you can also use Land visualizations to quickly get at the same answer.



Calculate total mutation burden of every sample in TCGALand

The number of identified mutations in cancer samples can vary wildly, but some tumors tend to aggregate widespread alterations. You can query TCGALand to generate a SampleSet of every sample in TCGALand, containing per-sample mutation status.


Calculate average mutation burden in each tumor in TCGALand

After summarizing how many total mutations occur in each sample of TCGALand, you can use Array Studio's summary functions to calculate and visualize the mutation frequency, and most common base changes, in each tumor.


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